Comparative genomics identifies candidate genes for infectious salmon anemia (ISA) resistance in Atlantic salmon (Salmo salar)

Abstract

Infectious salmon anemia (ISA) has been described as the hoof and mouth disease of salmon farming. ISA is caused by a lethal and highly communicable virus, which can have a major impact on salmon aquaculture, as demonstrated by an outbreak in Chile in 2007. A quantitative trait locus (QTL) for ISA resistance has been mapped to three microsatellite markers on linkage group (LG) 8 (Chr 15) on the Atlantic salmon genetic map. We identified bacterial artificial chromosome (BAC) clones and three fingerprint contigs from the Atlantic salmon physical map that contains these markers. We made use of the extensive BAC end sequence database to extend these contigs by chromosome walking and identified additional two markers in this region. The BAC end sequences were used to search for conserved synteny between this segment of LG8 and the fish genomes that have been sequenced. An examination of the genes in the syntenic segments of the tetraodon and medaka genomes identified candidates for association with ISA resistance in Atlantic salmon based on differential expression profiles from ISA challenges or on the putative biological functions of the proteins they encode. One gene in particular, HIV-EP2/MBP-2, caught our attention as it may influence the expression of several genes that have been implicated in the response to infection by infectious salmon anemia virus (ISAV). Therefore, we suggest that HIV-EP2/MBP-2 is a very strong candidate for the gene associated with the ISAV resistance QTL in Atlantic salmon and is worthy of further study.

Fig.1

Schematic representation of the genetic map of Atlantic salmon Chr15 (LG8) showing the ISA QTL region identified by Moen et al. (2004a, 2007) and the corresponding syntenic regions of medaka LG24

Fig. 2

A screenshot from www.asalbase.org that shows the annotated genes and transcripts from 23,300k–23,900k of medaka LG24 as well as the Atlantic salmon BAC end sequences that align with them. This region also contains one of the microsatellites, BHMS177, associated with the ISA resistance QTL (Moen et al. 2007) and three additional markers, Ssa0821BSFU, Ssa0130ECIG, and Ssa0578BSFU, that are tightly linked to BHMS177 (Danzmann et al. ; Phillips et al. 2009)